Possible recombination between two variants of concern in a COVID-19 patient

Yaqing He; Wentai Ma; Shengyuan Dang; Long Chen; Renli Zhang; Shujiang Mei; Xinyi Wei; Qiuying Lv; Bo Peng; Jiancheng Chen; Dongfeng Kong; Ying Sun; Xiujuan Tang; Weihua Wu; Zhigao Chen; Shimin Li; Jia Wan; Xuan Zou; Mingkun Li; Tiejian Feng; Lili Ren; Jianwei Wang

doi:10.1080/22221751.2022.2032375

Possible recombination between two variants of concern in a COVID-19 patient

Emerg Microbes Infect. 2022 Dec;11(1):552-555. doi: 10.1080/22221751.2022.2032375.

Authors

Yaqing He^{1

2}, Wentai Ma^{3

4}, Shengyuan Dang⁵, Long Chen^{1

2}, Renli Zhang^{1

2}, Shujiang Mei^{1

2}, Xinyi Wei^{1

2}, Qiuying Lv^{1

2}, Bo Peng^{1

2}, Jiancheng Chen^{1

2}, Dongfeng Kong^{1

2}, Ying Sun^{1

2}, Xiujuan Tang^{1

2}, Weihua Wu^{1

2}, Zhigao Chen^{1

2}, Shimin Li^{1

2}, Jia Wan^{1

2}, Xuan Zou^{1

2}, Mingkun Li^{3

4

6}, Tiejian Feng^{1

2}, Lili Ren^{5

7}, Jianwei Wang^{5

7}

Affiliations

¹ Shenzhen Research Center for Communicable Disease Control and Prevention Chinese Academy of Medical Sciences, Shenzhen, People's Republic of China.
² Center for Disease Control and Prevention, Shenzhen, People's Republic of China.
³ Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, People's Republic of China.
⁴ University of Chinese Academy of Sciences, Beijing, People's Republic of China.
⁵ National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China.
⁶ Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, People's Republic of China.
⁷ Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.

Abstract

We identified an individual who was coinfected with two SARS-CoV-2 variants of concern, the Beta and Delta variants. The ratio of the relative abundance between the two variants was maintained at 1:9 (Beta:Delta) in 14 days. Furthermore, possible evidence of recombinations in the Orf1ab and Spike genes was found.

Keywords: SARS-CoV-2; coinfection; intra-host single nucleotide variations; recombination.

Publication types

Letter

MeSH terms

COVID-19*
Humans
Recombination, Genetic
SARS-CoV-2*
Spike Glycoprotein, Coronavirus / genetics

Substances

Spike Glycoprotein, Coronavirus

Supplementary concepts

SARS-CoV-2 variants

Grants and funding

This research was supported by the Non-profit Central Research Institute Fund of Chinese Academy of Medical Science (APL211276910010201002008), National Natural Science Foundation of China (82161148009), Natural Science Foundation of Beijing, China (Z190017), Shenzhen Science and Technology Innovation Commission Key project (JSGG20200225152648408), Shenzhen Key Medical Discipline Construction Fund (SZXK064), the Key Project of Shenzhen Science and Technology Innovation Commission (KCXFZ2020020110061900).